Rules ordering scallop boats to report catches from Manx waters to an Isle of Man port have come into force, despite the Scottish government's concerns.
The rules were imposed over concerns about the accuracy of catch reports.
Scotland's Rural Economy Secretary Fergus Ewing said the imposition meant he had "no option" but to consider a dispute resolution process.
Manx Fisheries Minister Geoffrey Boot said the rules had been modified to make provision for British vessels.
Mr Ewing said the scallop industry was worth £3m annually in Scotland and his government had made it "consistently clear that these moves would breach existing fisheries agreements and would detrimentally affect Scottish fishermen".
He said the Manx administration had "not listened to our alternatives or our concerns [so] I have no option but to consider invoking the dispute resolution process as set out in the Fisheries Management Agreement (FMA)".
Dumfries and Galloway Council has previously said the stricter rules could "potentially put at risk" 300 jobs.
An Isle of Man government spokesman said it did not believe it had breached the FMA.
He said the measures, which cover both British and Manx vessels, were "urgently required to preserve declining stocks", adding that there were strong indications from catch records that some boats were taking more fish than they were entitled to.
Mr Boot said his government had taken account of Mr Ewing's concerns and modified arrangements, so that British vessels which only fished in Manx waters could return to their home ports and report their catches electronically.
The government spokesman said the king scallop industry is worth £12m annually to the Manx economy and the government continue to engage in dialogue with FMA partners to further assess the impact of the new rules.